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- PDB-9hs3: Crystal structure of the Escherichia coli nucleosidase PpnN (E264... -

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Basic information

Entry
Database: PDB / ID: 9hs3
TitleCrystal structure of the Escherichia coli nucleosidase PpnN (E264A, pppGpp form)
ComponentsPyrimidine/purine nucleotide 5'-monophosphate nucleosidase
KeywordsHYDROLASE / nucleosidase / pppGpp / GMP
Function / homology
Function and homology information


inosinate nucleosidase activity / pyrimidine-5'-nucleotide nucleosidase activity / pyrimidine-5'-nucleotide nucleosidase / AMP nucleosidase / AMP nucleosidase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / guanosine tetraphosphate binding / protein homotetramerization / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
: / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, C-terminal domain / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, N-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase PpnN-like superfamily / Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases / : / LOG family / Possible lysine decarboxylase
Similarity search - Domain/homology
Chem-0O2 / 5-O-phosphono-alpha-D-ribofuranose / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBaerentsen, R.L. / Brodersen, D.E.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0028072 Denmark
Novo Nordisk FoundationNNF18OC0030646 Denmark
CitationJournal: Structure / Year: 2025
Title: Catalytic mechanism and differential alarmone regulation of a conserved stringent nucleosidase
Authors: Baerentsen, R.L. / Kronborg, K. / Brodersen, D.E. / Zhang, Y.E.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
B: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
C: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
D: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,30212
Polymers205,6494
Non-polymers3,6538
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-27 kcal/mol
Surface area67390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.919, 156.919, 224.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase / AMP nucleosidase / CMP nucleosidase / GMP nucleosidase / IMP nucleosidase / UMP nucleosidase / dTMP ...AMP nucleosidase / CMP nucleosidase / GMP nucleosidase / IMP nucleosidase / UMP nucleosidase / dTMP nucleosidase


Mass: 51412.262 Da / Num. of mol.: 4 / Mutation: E264A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ppnN, ygdH, b2795, JW2766 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0ADR8, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, pyrimidine-5'-nucleotide nucleosidase, AMP nucleosidase
#2: Sugar
ChemComp-HSX / 5-O-phosphono-alpha-D-ribofuranose / 5-O-phosphono-alpha-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-0O2 / guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)


Mass: 683.140 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H18N5O20P5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density meas: 203888 Mg/m3 / Density % sol: 63.71 % / Description: octahedral
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 6 mg/ml 0.4 KNa tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 3.4→47.42 Å / Num. obs: 39210 / % possible obs: 99.83 % / Redundancy: 2 % / Biso Wilson estimate: 101.82 Å2 / CC1/2: 0.98 / CC star: 0.99 / Rrim(I) all: 0.18 / Net I/σ(I): 6.92
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 1.01 % / Num. unique obs: 3526 / CC1/2: 0.52 / CC star: 0.83 / Rrim(I) all: 1.11 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→47.42 Å / SU ML: 0.5556 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7227
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2779 396 1.01 %
Rwork0.2205 38814 -
obs0.2211 39210 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.78 Å2
Refinement stepCycle: LAST / Resolution: 3.4→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14181 0 56 17 14254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014314514
X-RAY DIFFRACTIONf_angle_d1.42519678
X-RAY DIFFRACTIONf_chiral_restr0.07552179
X-RAY DIFFRACTIONf_plane_restr0.01172552
X-RAY DIFFRACTIONf_dihedral_angle_d9.98681992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.890.3491300.317612691X-RAY DIFFRACTION99.67
3.89-4.90.28951300.220712842X-RAY DIFFRACTION99.95
4.9-47.420.24651360.186213281X-RAY DIFFRACTION99.95

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